Alternative GHA structure for nf-core/modules #28
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: test | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [master] | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [master] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| Prettier: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Install NodeJS | |
| uses: actions/setup-node@v3 | |
| - name: Install Prettier | |
| run: npm install -g prettier | |
| - name: Run Prettier --check | |
| run: prettier --check . | |
| EditorConfig: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-node@v3 | |
| - name: Install editorconfig-checker | |
| run: npm install -g editorconfig-checker | |
| - name: Run ECLint check | |
| run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) | |
| pytest-changes: | |
| name: pytest-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose matched filters as job 'modules' output variable | |
| modules: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: dorny/paths-filter@v2 | |
| id: filter | |
| with: | |
| filters: "tests/config/pytest_modules.yml" | |
| nf-core-lint: | |
| runs-on: ubuntu-20.04 | |
| name: nf-core-lint | |
| needs: [pytest-changes] | |
| if: needs.pytest-changes.outputs.modules != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"] | |
| exclude: | |
| - tags: "nf-test" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.x" | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.x" | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - name: Install nf-core tools | |
| run: python -m pip install nf-core | |
| - name: Install Nextflow | |
| env: | |
| CAPSULE_LOG: none | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Lint ${{ matrix.tags }} | |
| run: nf-core modules lint ${{ matrix.tags }} | |
| # HACK | |
| if: startsWith( matrix.tags, 'subworkflow' ) != true | |
| - uses: actions/cache@v3 | |
| with: | |
| path: /usr/local/bin/nextflow | |
| key: ${{ runner.os }} | |
| restore-keys: | | |
| ${{ runner.os }} | |
| pytest: | |
| runs-on: ubuntu-20.04 | |
| name: pytest | |
| needs: [pytest-changes] | |
| if: needs.changes.outputs.modules != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"] | |
| profile: ["docker", "singularity", "conda"] | |
| exclude: | |
| - tags: "nf-test" | |
| - profile: "conda" | |
| tags: annotsv | |
| - profile: "conda" | |
| tags: cellpose | |
| - profile: "conda" | |
| tags: mcquant | |
| - profile: "conda" | |
| tags: bases2fastq | |
| - profile: "conda" | |
| tags: backsub | |
| - profile: "conda" | |
| tags: basicpy | |
| - profile: "conda" | |
| tags: bcl2fastq | |
| - profile: "conda" | |
| tags: bclconvert | |
| - profile: "conda" | |
| tags: cellranger/count | |
| - profile: "conda" | |
| tags: cellranger/mkfastq | |
| - profile: "conda" | |
| tags: cellranger/mkgtf | |
| - profile: "conda" | |
| tags: cellranger/mkref | |
| - profile: "conda" | |
| tags: cellranger/mkvdjref | |
| - profile: "conda" | |
| tags: cellranger/multi | |
| - profile: "conda" | |
| tags: cellranger/vdj | |
| - profile: "conda" | |
| tags: coreograph | |
| - profile: "conda" | |
| tags: deepcell/mesmer | |
| - profile: "conda" | |
| tags: deepvariant | |
| - profile: "conda" | |
| tags: fastk/fastk | |
| - profile: "conda" | |
| tags: fastk/histex | |
| - profile: "conda" | |
| tags: fastk/merge | |
| - profile: "conda" | |
| tags: fcs/fcsadaptor | |
| - profile: "conda" | |
| tags: fcs/fcsgx | |
| - profile: "conda" | |
| tags: gatk4/baserecalibratorspark | |
| - profile: "conda" | |
| tags: gatk4/cnnscorevariants | |
| - profile: "conda" | |
| tags: gatk4/determinegermlinecontigploidy | |
| - profile: "conda" | |
| tags: gatk4/germlinecnvcaller | |
| - profile: "conda" | |
| tags: gatk4/markduplicatesspark | |
| - profile: "conda" | |
| tags: gatk4/postprocessgermlinecnvcalls | |
| - profile: "conda" | |
| tags: genescopefk | |
| - profile: "conda" | |
| tags: ilastik/multicut | |
| - profile: "conda" | |
| tags: ilastik/pixelclassification | |
| - profile: "conda" | |
| tags: imputeme/vcftoprs | |
| - profile: "conda" | |
| tags: merquryfk/katcomp | |
| - profile: "conda" | |
| tags: merquryfk/katgc | |
| - profile: "conda" | |
| tags: merquryfk/merquryfk | |
| - profile: "conda" | |
| tags: merquryfk/ploidyplot | |
| - profile: "conda" | |
| tags: mitohifi/findmitoreference | |
| - profile: "conda" | |
| tags: scimap/mcmicro | |
| - profile: "conda" | |
| tags: sentieon/applyvarcal | |
| - profile: "conda" | |
| tags: sentieon/bwaindex | |
| - profile: "conda" | |
| tags: sentieon/bwamem | |
| - profile: "conda" | |
| tags: sentieon/dedup | |
| - profile: "conda" | |
| tags: sentieon/gvcftyper | |
| - profile: "conda" | |
| tags: sentieon/haplotyper | |
| - profile: "conda" | |
| tags: sentieon/varcal | |
| - profile: "conda" | |
| tags: spaceranger/count | |
| - profile: "conda" | |
| tags: spaceranger/mkgtf | |
| - profile: "conda" | |
| tags: spaceranger/mkref | |
| - profile: "conda" | |
| tags: universc | |
| - profile: "singularity" | |
| tags: universc | |
| - profile: "singularity" | |
| tags: gatk4/determinegermlinecontigploidy | |
| - profile: "conda" | |
| tags: subworkflows/bcl_demultiplex | |
| - profile: "conda" | |
| tags: subworkflows/fasta_clean_fcs | |
| - profile: "conda" | |
| tags: islandpath | |
| env: | |
| NXF_ANSI_LOG: false | |
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.x" | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pytest-workflow cryptography | |
| - uses: actions/cache@v3 | |
| with: | |
| path: /usr/local/bin/nextflow | |
| key: ${{ runner.os }} | |
| restore-keys: | | |
| ${{ runner.os }}-nextflow- | |
| - name: Install Nextflow | |
| env: | |
| CAPSULE_LOG: none | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.7.1 | |
| - name: Set up miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| channels: conda-forge,bioconda,defaults | |
| python-version: ${{ matrix.python-version }} | |
| - name: Conda setup | |
| if: matrix.profile == 'conda' | |
| run: | | |
| conda clean -a | |
| conda install -n base conda-libmamba-solver | |
| conda config --set solver libmamba | |
| # Set up secrets | |
| - name: Set up nextflow secrets | |
| if: env.SENTIEON_LICENSE_BASE64 != null | |
| run: | | |
| nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }} | |
| SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d) | |
| SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d) | |
| SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") | |
| SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0) | |
| nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64 | |
| # Test the module | |
| - name: Run pytest-workflow | |
| # only use one thread for pytest-workflow to avoid race condition on conda cache. | |
| run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt-get update > /dev/null | |
| sudo apt-get install bat > /dev/null | |
| batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | |
| - name: Setting global variables | |
| uses: actions/github-script@v6 | |
| id: parsed | |
| with: | |
| script: | | |
| return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"') | |
| result-encoding: string | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }} | |
| path: | | |
| /home/runner/pytest_workflow_*/*/.nextflow.log | |
| /home/runner/pytest_workflow_*/*/log.out | |
| /home/runner/pytest_workflow_*/*/log.err | |
| /home/runner/pytest_workflow_*/*/work | |
| !/home/runner/pytest_workflow_*/*/work/conda | |
| !/home/runner/pytest_workflow_*/*/work/singularity | |
| nf-test-changes: | |
| name: nf-test-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose matched filters as job 'modules' output variable | |
| modules: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: dorny/paths-filter@v2 | |
| id: filter | |
| with: | |
| filters: "tests/config/nftest_modules.yml" | |
| nf-test: | |
| runs-on: ubuntu-20.04 | |
| name: nf-test | |
| needs: [nf-test-changes] | |
| if: needs.nf-test-changes.outputs.modules != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"] | |
| profile: ["docker", "singularity", "conda"] | |
| exclude: | |
| - tags: "nf-test" | |
| - profile: "conda" | |
| tags: annotsv | |
| - profile: "conda" | |
| tags: bases2fastq | |
| - profile: "conda" | |
| tags: bcl2fastq | |
| - profile: "conda" | |
| tags: bclconvert | |
| - profile: "conda" | |
| tags: cellranger/count | |
| - profile: "conda" | |
| tags: cellranger/mkfastq | |
| - profile: "conda" | |
| tags: cellranger/mkgtf | |
| - profile: "conda" | |
| tags: cellranger/mkref | |
| - profile: "conda" | |
| tags: deepvariant | |
| - profile: "conda" | |
| tags: ensemblvep/vep | |
| - profile: "conda" | |
| tags: fastk/fastk | |
| - profile: "conda" | |
| tags: fastk/histex | |
| - profile: "conda" | |
| tags: fastk/merge | |
| - profile: "conda" | |
| tags: fcs/fcsadaptor | |
| - profile: "conda" | |
| tags: fcs/fcsgx | |
| - profile: "conda" | |
| tags: gatk4/cnnscorevariants | |
| - profile: "conda" | |
| tags: gatk4/determinegermlinecontigploidy | |
| - profile: "conda" | |
| tags: genescopefk | |
| - profile: "conda" | |
| tags: ilastik/multicut | |
| - profile: "conda" | |
| tags: ilastik/pixelclassification | |
| - profile: "conda" | |
| tags: imputeme/vcftoprs | |
| - profile: "conda" | |
| tags: merquryfk/katcomp | |
| - profile: "conda" | |
| tags: merquryfk/katgc | |
| - profile: "conda" | |
| tags: merquryfk/merquryfk | |
| - profile: "conda" | |
| tags: merquryfk/ploidyplot | |
| - profile: "conda" | |
| tags: sentieon/bwaindex | |
| - profile: "conda" | |
| tags: sentieon/bwamem | |
| - profile: "conda" | |
| tags: universc | |
| - profile: "singularity" | |
| tags: universc | |
| - profile: "conda" | |
| tags: subworkflows/vcf_annotate_ensemblvep | |
| env: | |
| NXF_ANSI_LOG: false | |
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/cache@v3 | |
| with: | |
| path: /usr/local/bin/nextflow | |
| key: ${{ runner.os }} | |
| restore-keys: | | |
| ${{ runner.os }}-nextflow- | |
| - name: Install Nextflow | |
| env: | |
| CAPSULE_LOG: none | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Cache nf-test installation | |
| id: cache-software | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/local/bin/nf-test | |
| /home/runner/.nf-test/nf-test.jar | |
| key: ${{ runner.os }}-nftest | |
| - name: Install nf-test | |
| if: steps.cache-software.outputs.cache-hit != 'true' | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.7.1 | |
| - name: Set up miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| channels: conda-forge,bioconda,defaults | |
| python-version: ${{ matrix.python-version }} | |
| - name: Conda setup | |
| if: matrix.profile == 'conda' | |
| run: | | |
| conda clean -a | |
| conda install -n base conda-libmamba-solver | |
| conda config --set solver libmamba | |
| # Set up secrets | |
| - name: Set up nextflow secrets | |
| if: env.SENTIEON_LICENSE_BASE64 != null | |
| run: | | |
| nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }} | |
| SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d) | |
| SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d) | |
| SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") | |
| SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0) | |
| nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64 | |
| # Test the module | |
| - name: Run nf-test | |
| run: | | |
| nf-test test \ | |
| --profile=${{ matrix.profile }} \ | |
| --tag ${{ matrix.tags }} \ | |
| --tap=test.tap | |
| - uses: pcolby/tap-summary@v1 | |
| with: | |
| path: >- | |
| test.tap | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| needs: [Prettier, EditorConfig, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test] | |
| if: always() | |
| steps: | |
| - name: All tests ok | |
| if: | | |
| always() && | |
| !contains(needs.*.result, 'failure') && | |
| !contains(needs.*.result, 'cancelled') | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 |